# Patent

## Title
Production of itaconic acid

## Abstract

The invention relates to the production of itaconic acid in micro-organisms by introducting into a suitable host cell a gene coding for the enzyme cis-aconitic acid decarboxylase, preferably derived from A. terreus. Further part of the invention are host cells, preferably from A. niger, provided with the above mentioned genes.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is the national phase of PCT application PCT/NL2008/050499 having an international filing date of 21 Jul. 2008, which claims benefit of European application No. 07112895.3 filed 20 Jul. 2007. The contents of the above patent applications are incorporated by reference herein in their entirety.
REFERENCE TO SEQUENCE LISTING SUBMITTED VIA EFS-WEB
The entire content of the following electronic submission of the sequence listing via the USPTO EFS-WEB server, as authorized and set forth in MPEP §1730 II.B.2(a)(C), is incorporated herein by reference in its entirety for all purposes. The sequence listing is identified on the electronically filed text file as follows:












File Name
Date of Creation
Size (bytes)







313632008300Seqlist.txt
Jul. 19, 2012
121,828 bytes









The invention relates to the field of microbial production, more specifically production of itaconic acid (itaconate), more specifically production of itaconate in micro-organisms.
Production and metabolism of itaconic acid in microbial cells has been studied extensively for several decades (Calam, C. T. et al., 1939, Thom. J. Biochem., 33:1488-1495; Bentley, R. and Thiessen, C. P., 1956, J. Biol. Chem. 226:673-720; Cooper, R. A. and Kornberg, H. L., 1964, Biochem. J., 91:82-91; Bonnarme, P. et al., 1995, J. Bacteriol. 117:3573-3578; Dwiarti, L. et al., 2002, J. Biosci. Bioeng. 1:29-33), but the metabolic pathway for itaconic acid has not been unequivocally established (Wilke, Th. and Vorlop, K.-D., 2001, Appl. Microbiol. Biotechnol. 56:289-295; Bonnarme, P. et al., 1995, J. Bacteriol. 177:3573-3578). Two complicating factors in this respect are that the biosynthesis route for itaconic acid is thought to occur both in the cytosol and the mitochondria (Jaklitsch, W. M. et al., 1991, J. Gen. Microbiol. Appl. 6:51-61) and that aconitase, the enzyme that interconverts citric acid into cis-aconitate, and vice versa, and other enzymes in the metabolic pathway have been found to be present in many isoforms in microbial cells.
Production of itaconic acid is now commercially achieved in Aspergillus terreus, which has physiological similarity to A. niger and A. oryzae. However, these latter two accumulate citric acid, due to the absence of cis-aconic acid decarboxylase (CAD) activity. Substrates used by these fungi include mono- and disaccharides, such as glucose, sucrose and fructose and starches, as they exist in forms which are degradable by the micro-organism, and molasses. Recently, it has been discovered that also glycerol is a useful substrate in itaconic acid production by A. terreus (U.S. Pat. No. 5,637,485).
The general scheme currently envisioned for itaconic acid biosynthesis is given in FIG. 1, wherein clearly the existence of the biosynthetic route both in the cytosol and the mitochondria is depicted and the putative connection between these two compartments. At several point of this scheme possibilities exist to try to improve the existing commercial production of itaconic acid in micro-organisms.
SUMMARY OF THE INVENTION
The present inventors now have elucidated the gene coding for the cis-aconitate decarboxylase enzyme and have found that overexpression of the cis-aconitate decarboxylase gene from Aspergillus is able to boost the production of itaconic acid. Accordingly, the invention comprises a method for the production of itaconic acid comprising overexpression of a gene coding for the enzyme cis-aconitic acid decarboxylase (CAD) in a suitable host cell. Preferably said gene is derived from Aspergillus terreus. The suitable host cell is preferably an Aspergillus niger or A. terreus host cell. According to a further preferred embodiment, the CAD gene is under control of its own or other promoters.
Another embodiment of the present invention is formed by a host cell wherein a gene coding for the enzyme cis-aconitic acid decarboxylase is introduced, preferably wherein said enzyme is derived from Aspergillus terreus. Said host cell preferably is a host cell selected from filamentous fungi, yeasts and bacteria, more preferably from Escherichia coli, Aspergillus niger and citrate- or lovastatin-producing hosts.
Further, the invention pertains to the use of the enzyme cis-aconitic acid decarboxylase for the production of itaconic acid in a suitable host cell.
Also comprised in the invention is a method as described above, wherein the production and/or transport of itaconic acid is further increased by increasing the intracellular itaconic acid, using at least one but preferably a combination of the following methods: 1. overexpression of a gene coding for a protein capable of transporting di/tricarboxylate, preferably cis-aconitate, citrate or isocitrate, from the mitochondrion to the cytosol, more preferably the dicarboxylate transporter encoded by the nucleic acid sequence of ATEG—09970.1 (SEQ ID NO:19) (see co-pending application EP 08151584); 2. a method as described above, wherein the activity of a regulator protein that comprises a zinc finger and a fungal specific transcription factor domain is modulated. Preferably said regulator protein is the protein encoded by the nucleic acid sequence of ATEG—09969.1 (SEQ ID NOS:17-18), located in the same gene cluster as the transporter of the invention; 3 overexpression of a nucleic acid sequence encoding an itaconate transporting Major Facilitator Superfamily Transporter (MFST) gene sequence (hereinafter “the itaconate transporter”). Preferably said nucleic acid comprises the ATEG—09972.1 sequence of Aspergillus terreus (SEQ ID NO:20) or a nucleic acid that shares more than about 70%, preferably more than about 80%, preferably more than about 90% sequence identity with the sequence of ATEG—09972.1 (SEQ ID NO:20) (as described in co-pending application EP 08152332).



LEGENDS TO THE FIGURES
FIG. 1: Postulated biosynthesis route(s) for itaconic acid in A. terreus. 1, Citrate synthase; 2, Aconitase; 3, cis-aconitic acid decarboxylase (itaconate-forming); 4, cis-aconitic acid decarboxylase (citraconate-forming); 5, citraconate isomerase; 6, mitochondrial dicarboxylate-tricarboxylate antiporter; 7, mitochondrial tricarboxylate transporter; 8, dicarboxylate transporter; 9, 2-methylcitrate dehydratase.
FIG. 2: Genomic nucleic acid sequence (SEQ ID NO:1) (A) and encoded amino acid sequence (SEQ ID NO:2) (B) of the A. terreus CAD gene. The depicted genomic sequence also shows 500 nucleotides 5′ to the ATG start of the coding sequence. Further, the genomic sequence has a small intron.
FIG. 3: Sequence comparison of the CAD protein from A. terreus and several homologous proteins (see detailed description for the species of which the NCBI accession number is given in the figure). (SEQ ID NOS:2, 3, 15, 4, 5, 6, 7, 8, 9, 10, 13, 11, 12, and 14, in order of appearance)
FIG. 4: Separation of proteins from a G25 chromatography desalted 35-60% ammonium sulfate pellet of cell extracts of A. terreus on an anion exchange Source Q15 column. Blue=OD280, black=% solution B (1 M NaCl) salt B in gradient, red=conductivity, green=CAD activity.
FIG. 5: SDS-PAGE of cell extract of recombinant E. coli containing the CAD gene on the pET52 expression vector. (+) and (−), with and without IPTG induction; M, protein markers.
FIG. 6: Overview of Aspergillus terreus genome segment with the cluster of genes involved in production of itaconic acid and lovastatin ranging from ATEG 09961.1-ATEG 09975.1. The cluster contains the cis-aconitate decarboxylase (ATEG—09971.1) and the mitochondrial tricarboxylate transporter (ATEG—9970.1).



DETAILED DESCRIPTION OF THE INVENTION
“Fungi” are herein defined as eukaryotic microorganisms and include all species of the subdivision Eumycotina (Alexopoulos, C. J., 1962, In: Introductory Mycology, John Wiley & Sons, Inc., New York). The term fungus thus includes both filamentous fungi and yeast. “Filamentous fungi” are herein defined as eukaryotic microorganisms that include all filamentous forms of the subdivision Eumycotina. These fungi are characterized by a vegetative mycelium composed of chitin, cellulose, and other complex polysaccharides. The filamentous fungi used in the present invention are morphologically, physiologically, and genetically distinct from yeasts. Vegetative growth by filamentous fungi is by hyphal elongation and carbon catabolism of most filamentous fungi are obligately aerobic. “Yeasts” are herein defined as eukaryotic microorganisms and include all species of the subdivision Eumycotina that predominantly grow in unicellular form. Yeasts may either grow by budding of a unicellular thallus or may grow by fission of the organism.
The term “fungal”, when referring to a protein or nucleic acid molecule thus means a protein or nucleic acid whose amino acid or nucleotide sequence, respectively, naturally occurs in a fungus.
One of the key enzymes in the biosynthetic pathway for itaconic acid is cis-aconitic acid decarboxylase (CAD). Purification and characterization of said enzyme from Aspergillus terreus has been reported (Dwiarti et al., 2002, J. Biosc. Bioeng. 94(1):29-33). The present inventors have followed the purification protocol and moreover have applied a transcriptomics approach. Using these approaches they have been able to identify the gene coding for CAD. The genomic sequence, along with the encoded amino acid sequence, is indicated in FIG. 2.
Also comprised in the invention are homologous proteins that are derived from other micro-organisms (also called orthologues). It will be clear for a person skilled in the art that on basis of the nucleotide sequences coding for the CAD enzyme of A. terreus as depicted in FIG. 2, orthologues from other micro-organism species can be easily found through database searching in NCBI GenBank based on sequence similarity and alignment analysis using minimal gap size in the alignment.
Also part of the invention are nucleotide sequences which are conservatively modified variants of the above mentioned sequences or polymorphic variants thereof. Those of skill in the art will recognize that the degeneracy of the genetic code allows for a plurality of polynucleotides to encode the identical amino acid. Such “silent variations” can be used, for example, to selectively hybridize and detect allelic variants of the nucleotide sequences of the present invention. Additionally, the present invention provides isolated nucleotide sequences comprising one or more polymorphic (allelic) variants of the above nucleotide sequences. Further part of the invention are polynucleotides still coding for a protein which has a biological function identical to the function of the CAD enzyme, which are the product of amplification from a nucleotide library using primer pairs which selectively hybridize under stringent conditions to loci within the above mentioned nucleotide sequences. The primer length in nucleotides is selected from the group of integers consisting of from at least 15 to 50. Those of skill in the art will recognize that a lengthened primer sequence can be employed to increase specificity of binding (i.e. annealing) to a target sequence. Stringent conditions in this respect means a reaction at a temperature of between 60° C. and 65° C. in 0.3 strength citrate buffered saline containing 0.1% SDS followed by rinsing at the same temperature with 0.3 strength citrate buffered saline containing 0.1% SDS.
Thus, also part of the invention are polynucleotides which selectively hybridize, under selective hybridization conditions, to one or more of the above discussed nucleotide sequences, and which code for an amino acid sequence which has a biological function similar to the function of the CAD enzyme disclosed in the present invention. Another way to indicate hybridization potential is on sequence identity. In this sense, the present invention provides also for nucleotide sequences which have a percentage of identity related to the above mentioned sequences of 40% to 95%. Thus, for example, the percentage of identity can be at least, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%. Sequence identity on nucleotide sequences can be calculated by using the BLASTN computer program (which is publicly available, for instance through the National Center for Biotechnological Information, accessible via the internet on http://www.ncbi.nlm.nih.gov/) using the default settings of 11 for wordlength (W), 10 for expectation (E), 5 as reward score for a pair of matching residues (M), −4 as penalty score for mismatches (N) and a cutoff of 100.
Similarly, the homology can be calculated on basis of the amino acid sequence of the enzyme encoded by said nucleotide sequences. For amino acids, the sequence identity can be calculated through the BLASP computer program (also available through http://www.ncbi.nlm.nih.gov/). On the amino acid level homologues or orthologues are defined as amino acid sequences having a biological function similar to the CAD enzyme (i.e. active in the decarboxylation of cis-acotinic acid) and having a sequence identity of at least 50%, preferably at least 55%, preferably at least 60%, more preferably at least 70%, more preferably at least 80%, more preferably at least 90%, more preferably at least 95% to the amino acid sequence of the A. terreus CAD enzyme as depicted in FIG. 2B.
Examples of such homologues (with NCBI numbers in brackets) are Aspergillus terreus (ATEG—09971 or XP—001209273 (SEQ ID NO:3)), Aspergillus terreus (ATEG—08909 or AAD34563 (SEQ ID NO:15) or XP—001217495 (SEQ ID NO:9)), Aspergillus terreus (ATEG—07260 or XP—001209946 (SEQ ID NO:16)), Aspergillus oryzae (BAE66063 (SEQ ID NO:4)), Aspergillus niger (XP—001393934 (SEQ ID NO:5)), Gibberella zeae (XP—391316 (SEQ ID NO:7)), Aspergillus niger (XP—001389415 (SEQ ID NO:6)), Pichia stipitis (XP—001383451 (SEQ ID NO:8)), Mycobacterium smegmatis (YP—891060 (SEQ ID NO:11)), Mycobacterium avium subsp. pratuberculosis (NP—961187 (SEQ ID NO:10)), Mycobacterium avium (YP—880968 (SEQ ID NO:13)), Salinispora arenicola (ZP—01648681 (SEQ ID NO:12)) and Salonispora tropica (YP—001161249 (SEQ ID NO:14)). For a sequence comparison of the sequences from these organisms with the CAD sequence of A. terreus (SEQ ID NO:2), see FIG. 3.
It further is contemplated that overexpression of the gene in a heterologous organism, which in nature does not or hardly produce itaconic acid, is able to provide such an organism with a functional pathway for expression of itaconic acid. Preferably such overexpression is accomplished in filamentous fungi, yeasts and/or bacteria, such as, but not limited to, Aspergillus sp., such as the fungi A. terreus, A. itaconicus and A. niger, Ustilago zeae, Ustilago maydis, Ustilago sp., Candida sp., Yarrowia lipolytica, Rhodotorula sp. and Pseudozyma Antarctica, the bacterium E. coli and the yeast Saccharomyces cerevisiae. Especially preferred are heterologous organisms in which the substrate cis-aconitate is available in the host organism. This cis-aconitate is formed from citric acid by either the enzyme aconitase or the enzyme 2-methylcitrate dehydratase, likely both in the cytosol and in the mitochondrion (see FIG. 1). It is submitted that this substrate is sufficiently available in Aspergillus strains since several aconitase-like genes have been identified on the genomes of the presently sequenced Aspergillus micro-organisms. Thus, other citric acid producing organisms, such as the above mentioned Yarrowia lipolytica, could be used for the overexpression of the CAD gene. It is further submitted that the CAD substrate cis-aconitate, or its precursor citrate, is available in large amounts in every cell, since it is part of the ubiquitous Krebs cycle. The production of itaconic acid can be further optimised by combining the overexpression of a CAD gene as described above, with overexpression of di/tricarboxylate transporters, capable of transporting, among others, cis-aconitate, citrate or isocitrate from the mitochondrion to the cytosol, preferably the gene encoded by the nucleic acid sequence of ATEG—09970.1 (SEQ ID NO:19). Overexpression of this transporter will lead to an increase in cis-aconitate in the cytosol, which can be further converted to itaconic acid.
Even further optimisation of the present invention can be achieved by modulating the activity of the regulator protein that comprises a zinc finger and a fungal specific transcription factor domain as can be found on the gene cluster that also comprises ATEG—09970 (SEQ ID NOS:19-20), wherein this regulator protein is indicated as ATEG—09969.1 (SEQ ID NO:18) (see FIG. 6). Further, overexpression of a nucleic acid sequence encoding an itaconate transporting Major Facilitator Superfamily Transporter (MFST) gene sequence (hereinafter “the itaconate transporter”) enhances the production/transport of itaconate as described herein. Preferably said nucleic acid comprises the ATEG—09972.1 sequence of Aspergillus terreus (SEQ ID NO:20) or a nucleic acid that shares more than about 70%, preferably more than about 80%, preferably more than about 90% sequence identity with the sequence of ATEG—09972.1 (SEQ ID NO:20) (as described in co-pending application EP 08152332).
Modulation of the activity of the (expression of the) regulator protein can be achieved by overexpression of a nucleic acid encoding said regulator protein, preferably the nucleic acid comprised in ATEG—09969.1 (as indicated in FIG. 6) when an increase in the regulator protein is intended. If a decrease in the amount of regulator protein is intended, expression of the gene can be inhibited by ways known in the art, such as anti-sense expression, sense co-suppression or RNA inhibition (RNAi).
Recently (see US 2004/0033570) it has also been established that the so-called D4B segment of Aspergillus terreus, which comprises amongst others the CAD gene as disclosed in FIG. 2, is responsible for the synthesis of lovastatin (see also FIG. 6). Thus, it is submitted that also these micro-organisms which are known to produce lovastatin would be suitable candidates for the production of itaconic acid. Such micro-organisms include Monascus spp. (such as M. ruber, M. purpureus, M. pilosus, M. vitreus and M. pubigerus), Penicillium spp. (such as P. citrinum, P. chrysogenum), Hypomyces spp., Doratomyces spp. (such as D. stemonitis), Phoma spp., Eupenicillium spp., Gymnoascus spp., Pichialabacensis, Candida cariosilog/licola, Paecilomyces virioti, Scopulariopsis brevicaulis and Trichoderma spp. (such as T. viride). Consequently also the CAD encoding part of the D4B segment and the enzyme with CAD activity for which it codes from these above-mentioned lovastatin producing micro-organisms are deemed to be suitable for use in the present invention.
Recombinant host cells can be obtained using methods known in the art for providing cells with recombinant nucleic acids. These include transformation, transconjugation, transfection or electroporation of a host cell with a suitable plasmid (also referred to as vector) comprising the nucleic acid construct of interest operationally coupled to a promoter sequence to drive expression. Host cells of the invention are preferably transformed with a nucleic acid construct as further defined below and may comprise a single but preferably comprises multiple copies of the nucleic acid construct. The nucleic acid construct may be maintained episomally and thus comprise a sequence for autonomous replication, such as an ARS sequence. Suitable episomal nucleic acid constructs may e.g. be based on the yeast 2μ or pKD1 (Fleer et al., 1991, Biotechnology 9: 968-975) plasmids. Preferably, however, the nucleic acid construct is integrated in one or more copies into the genome of the host cell. Integration into the host cell's genome may occur at random by illegitimate recombination but preferably the nucleic acid construct is integrated into the host cell's genome by homologous recombination as is well known in the art of fungal molecular genetics (see e.g. WO 90/14423, EP-A-0 481 008, EP-A-0 635 574 and U.S. Pat. No. 6,265,186).
Transformation of host cells with the nucleic acid constructs of the invention and additional genetic modification of the fungal host cells of the invention as described above may be carried out by methods well known in the art. Such methods are e.g. known from standard handbooks, such as Sambrook and Russel (2001) “Molecular Cloning: A Laboratory Manual (3rd edition), Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, or F. Ausubel et al, eds., “Current protocols in molecular biology”, Green Publishing and Wiley Interscience, New York (1987). Methods for transformation and genetic modification of fungal host cells are known from e.g. EP-A-0 635 574, WO 98/46772, WO 99/60102 and WO 00/37671.
In another aspect the invention relates to a nucleic acid construct comprising a nucleotide sequence encoding a CAD enzyme as defined above and used for transformation of a host cell as defined above. In the nucleic acid construct, the nucleotide sequence encoding the CAD protein preferably is operably linked to a promoter for control and initiation of transcription of the nucleotide sequence in a host cell as defined below. The promoter preferably is capable of causing sufficient expression of the CAD enzyme in the host cell. Promoters useful in the nucleic acid constructs of the invention include the promoter that in nature provides for expression of the CAD gene. Said promoter is comprised in the 500 nucleotides 5′ to the coding sequence of the CAD gene, as depicted in FIG. 2A. Further, both constitutive and inducible natural promoters as well as engineered promoters can be used. Promotors suitable to drive expression of the CAD gene in the hosts of the invention include e.g. promoters from glycolytic genes (e.g. from a glyceraldehyde-3-phosphate dehydrogenase gene), ribosomal protein encoding gene promoters, alcohol dehydrogenase promoters (ADH1, ADH4, and the like), promoters from genes encoding amylo- or cellulolytic enzymes (glucoamylase, TAKA-amylase and cellobiohydrolase). Other promoters, both constitutive and inducible and enhancers or upstream activating sequences will be known to those of skill in the art. The promoters used in the nucleic acid constructs of the present invention may be modified, if desired, to affect their control characteristics. Preferably, the promoter used in the nucleic acid construct for expression of the CAD gene is homologous to the host cell in which the CAD protein is expressed.
In the nucleic acid construct, the 3′-end of the nucleotide acid sequence encoding the CAD enzyme preferably is operably linked to a transcription terminator sequence. Preferably the terminator sequence is operable in a host cell of choice. In any case the choice of the terminator is not critical; it may e.g. be from any fungal gene, although terminators may sometimes work if from a non-fungal, eukaryotic, gene. The transcription termination sequence further preferably comprises a polyadenylation signal.
Optionally, a selectable marker may be present in the nucleic acid construct. As used herein, the term “marker” refers to a gene encoding a trait or a phenotype which permits the selection of, or the screening for, a host cell containing the marker. A variety of selectable marker genes are available for use in the transformation of fungi. Suitable markers include auxotrophic marker genes involved in amino acid or nucleotide metabolism, such as e.g. genes encoding ornithine-transcarbamylases (argB), orotidine-5′-decarboxylases (pyrG, URA3) or glutamine-amido-transferase indoleglycerol-phosphate-synthase phosphoribosyl-anthranilate isomerases (trpC), or involved in carbon or nitrogen metabolism, such e.g. niaD or facA, and antibiotic resistance markers such as genes providing resistance against phleomycin, bleomycin or neomycin (G418). Preferably, bidirectional selection markers are used for which both a positive and a negative genetic selection is possible. Examples of such bidirectional markers are the pyrG (URA3), facA and amdS genes. Due to their bidirectionality these markers can be deleted from transformed filamentous fungus while leaving the introduced recombinant DNA molecule in place, in order to obtain fungi that do not contain selectable markers. This essence of this MARKER GENE FREETM transformation technology is disclosed in EP-A-0 635 574, which is herein incorporated by reference. Of these selectable markers the use of dominant and bidirectional selectable markers such as acetamidase genes like the amdS genes of A. nidulans, A. niger and P. chrysogenum is most preferred. In addition to their bidirectionality these markers provide the advantage that they are dominant selectable markers that, the use of which does not require mutant (auxotrophic) strains, but which can be used directly in wild type strains.
Optional further elements that may be present in the nucleic acid constructs of the invention include, but are not limited to, one or more leader sequences, enhancers, integration factors, and/or reporter genes, intron sequences, centromers, telomers and/or matrix attachment (MAR) sequences. The nucleic acid constructs of the invention may further comprise a sequence for autonomous replication, such as an ARS sequence. Suitable episomal nucleic acid constructs may e.g. be based on the yeast 2μ or pKD1 (Fleer et al., 1991, Biotechnology 9: 968-975) plasmids. Alternatively the nucleic acid construct may comprise sequences for integration, preferably by homologous recombination (see e.g. WO98/46772). Such sequences may thus be sequences homologous to the target site for integration in the host cell's genome. The nucleic acid constructs of the invention can be provided in a manner known per se, which generally involves techniques such as restricting and linking nucleic acids/nucleic acid sequences, for which reference is made to the standard handbooks, such as Sambrook and Russel (2001) “Molecular Cloning: A Laboratory Manual (3rd edition), Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, or F. Ausubel et al, eds., “Current protocols in molecular biology”, Green Publishing and Wiley Interscience, New York (1987).
In a further aspect the invention relates to fermentation processes in which the transformed host cells of the invention are used for the conversion of a substrate into itaconic acid. A preferred fermentation process is an aerobic fermentation process. The fermentation process may either be a submerged or a solid state fermentation process.
In a solid state fermentation process (sometimes referred to as semi-solid state fermentation) the transformed host cells are fermenting on a solid medium that provides anchorage points for the fungus in the absence of any freely flowing substance. The amount of water in the solid medium can be any amount of water. For example, the solid medium could be almost dry, or it could be slushy. A person skilled in the art knows that the terms “solid state fermentation” and “semi-solid state fermentation” are interchangeable. A wide variety of solid state fermentation devices have previously been described (for review see, Larroche et al., “Special Transformation Processes Using Fungal Spores and Immobilized Cells”, Adv. Biochem. Eng. Biotech., (1997), Vol 55, pp. 179; Roussos et al., “Zymotis: A large Scale Solid State Fermenter”, Applied Biochemistry and Biotechnology, (1993), Vol. 42, pp. 37-52; Smits et al., “Solid-State Fermentation-A Mini Review, 1998), Agro-Food-Industry Hi-Tech, March/April, pp. 29-36). These devices fall within two categories, those categories being static systems and agitated systems. In static systems, the solid media is stationary throughout the fermentation process. Examples of static systems used for solid state fermentation include flasks, petri dishes, trays, fixed bed columns, and ovens. Agitated systems provide a means for mixing the solid media during the fermentation process. One example of an agitated system is a rotating drum (Larroche et al., supra). In a submerged fermentation process on the other hand, the transformed fungal host cells are fermenting while being submerged in a liquid medium, usually in a stirred tank fermenter as are well known in the art, although also other types of fermenters such as e.g. airlift-type fermenters may also be applied (see e.g. U.S. Pat. No. 6,746,862).
Preferred in the invention is a submerged fermentation process, which is performed fed-batch. This means that there is a continuous input of feed containing a carbon source and/or other relevant nutrients in order to improve itaconic acid yields. The input of the feed can, for example, be at a constant rate or when the concentration of a specific substrate or fermentation parameter falls below some set point.
EXAMPLES
Example 1
Purification of CAD
Spores 5×108 were inoculated into 100 ml medium (glucose 20 g/L (pre-culture), 100 g/L (production culture); 2.0 g/L NH4NO3; 0.08 g/L KH2PO4; 1 g/L MgSO4*7H2O; 10 g/L CaCl2*2H2O; 15 mg/L CuSO4*5H2O; 1.7 mg/L Fe(II)SO4*7H2O; pH 3.1) and incubated at 30° C. for 48 h on a rotary shaker at 250 rpm. Of the preculture 8 ml was used per 200 ml in 1 L Erlenmeyer flasks for the production culture. Then the mycelium was collected from the broth by filtration and washed with 0.2 M sodium phosphate buffer (pH 6.5). Batches of ±5 g were frozen in liquid nitrogen and stored at −80° C.
Twenty grams of mycelium obtained from 2 liter production culture was ground with a pestle under liquid nitrogen in a pre-chilled mortar. The mycelium powder was suspended in 160 ml of 0.2 M sodium phosphate (pH 6.5), 1 mM EDTA, 1 mM DTT, 1 mM PMSF and 1.0 μg/ml pepstatin A. The suspension was subsequently centrifuged for 10 minutes (10.000 g) at 4° C. After ammonium sulphate precipitation (35-60% saturation) the precipitated protein fraction was resuspended and desalted on a G25 gel filtration column in 16 ml of 50 mM sodium phosphate buffer (pH 6.5), 30% glycerol, 1 mM EDTA, 1 mM DTT and 1.0 μg/ml pepstatin A (CAD buffer). After desalting the pooled, protein containing fractions (high molecular weight material), were diluted with CAD buffer to ±38 ml and supplied to a 23 ml Source 15Q ion-exchange resin, packed in an HR 16/10 column. This column was eluted with a linear gradient of 0-0.6 M NaCl in 400 ml CAD buffer, followed by a gradient of 0.6-1 M NaCl in 60 ml CAD buffer with a speed of 6 ml/min. Fractions of 10 and 6 ml were collected and cooled on ice. Analysis showed that two fractions contained approximately 4.5 mg protein of which 2.6 mg CAD (purity±60%).
Approximately 4.5 ml of one of the fractions was desalted on a G25 gel filtration column, after which the desalted, high molecular weight material was bound to a 1 ml Source 15Q column in CAD buffer and subsequently eluted with a steep gradient of 1 M NaCl in CAD buffer. The eluted active fractions were pooled and applied to a 24 ml Superdex 75 (14 μm) resin, packed in an HR 10/30 column. The column was eluted with CAD buffer with 0.15 M NaCl, with a speed of 0.2 ml/min (see FIG. 4). The fractions showing the highest specific CAD activity were analyzed through gel electrophoresis using SDS-PAGE (8-16% gradient). An abundant band at approximately 55 kDa was observed. This band was isolated from the gel for N-terminal sequencing. For ESI/MS/MS analysis the gel was first blotted onto a PVDF membrane from which the 55 kDa protein band was subsequently isolated. N-terminal sequencing and MS/MS data both reveal the hypothetical protein from A. terreus, having homology to prpD (ATEG—09971).
Example 2
Enzymatic Activity Analysis
During the isolation as described in Example 1 the isolated fractions were subjected to enzymatic activity assays for determining the presence/activity of the CAD protein. A sample of the fractions was incubated at 37° C. for 30 min in 0.2 M sodium phosphate with 19 mM cis-aconitic acid at pH 6.2. The enzyme reaction was terminated by addition of strong acid (HCl to a final concentration of ±1 M). The following Table indicates the concentrations of itaconate in the samples and control samples (control samples are treated according to the above assay, but without addition of the substrate cis-aconitic acid to determine the background itaconate level).
Analysis was performed with a reversed phase HPLC, using a DevelosilTM 3 μm RP-Aqueous C30 140A column at a constant temperature of 25° C., with alution with 20 mM NaH2PO4, pH 2.25 and acetonitril. Detection was performed by UV 210 nm. Retention time of the cis-aconitate was 10.89 min, the trans-aconitic acid 16.11 min and itaconic acid 18.82 min.
















Itaconate
Control



sample
in μg/ml
itaconate




















Crude extract after grinding (total
239.7
35.8



volume 175 ml, 160 μl in assay)



Resuspended 35-60% ammonium
1296.7
17.1



sulphate fraction (total volume 16 ml,



160 μl in assay)



Desalted fractions prior to ion-
1092.9



exchange










Example 3
Construction of Micro-Array
An anonymous clone/EST-based array approach was taken according to the following scheme:




An A. terreus micro-array was made composed of a clone-based and an EST-based array.
Materials and Methods Construction Micro-Array
Isolation of Chromosomal DNA from A. terreus 
A. terreus was cultivated overnight in a shake flask in enriched minimal medium at 33° C. and 250 rpm. Enriched minimal medium (pH 5.5) is mineral medium (MM) supplemented with 0.5% yeast extract and 0.2% casamino acids. The composition of MM was: 0.07 M NaNO3, 7 mM KCl, 0.11 M KH2PO4, 2 mM MgSO4, and 1 ml/l of trace elements (1000*stock solution: 67 mM ZnSO4, 178 mM H3BO3, 25 mM MnCl2, 18 mM FeSO4, 71 mM CoCl2, 6.4 mM CuSO4, 6.2 mM Na2MoO4, 174 mM EDTA).
Mycelium was harvested after 22 hours and frozen in liquid nitrogen. Chromosomal DNA was isolated from 4.5 g mycelium following the protocol described below.

    
    
        Grind 0.5-1.0 g mycelium under liquid nitrogen using the membrane disrupter.
        Place polypropylene tubes (Greiner) with 1.5 ml water-saturated phenol, 1 ml TNS, 1 ml PAS and as ml 5×RNB in a water bath at 55° C., add the still frozen mycelium to the tubes and vortex every 20 seconds for totally 2-4 minutes.
        
            TNS: triisopropyl naphthalene sulphonic acid, 20 mg/ml in water, freshly prepared
            PAS: 4 aminosalisylic acid, 120 mg/ml in water, freshly prepared
            5×RNB: 60.55 g Tris, 36.52 g NaCl, 47.55 g EGTA in 500 ml water (pH=8.5)
        
        
        Add 1 ml sevag and vortex with intervals for another 1-2 minutes.
        Spin for 10 min. in the tabletop centrifuge at 4° C. at maximum velocity.
        Extract the water-phase once again with phenol-sevag and twice with sevag. GENTLY, AVOID SHEARING!
        Precipitate the DNA with 2 volumes ethanol. Spin directly for 10 min. in the tabletop centrifuge.
        Drain the tube, dry it with Kleenex and resuspend the pellet in 500 μl Tris/EDTA. Transfer to a microvial.
        Extract with phenol-sevag until interface stays clean. Then extract once with sevag.
        Precipitate with 2 volumes ice-cold ethanol, spin down and resuspend the pellet in 100-200, μl TE with 50 μg/ml RNase.

Construction of Clone-Based gDNA Library

The gDNA library was prepared as follows:

        Chromosomal A. terreus DNA was sheared into fragments of size 1.5-2.5 kb
        The sheared DNA was subsequently size fractionated, end-repaired (Lucigen), and ligated into blunt-end pSMART-HC-Amp vectors (Lucigen).
        The ligated constructs were transformed into E. coli DH 10b
        Colony PCR was performed on 96 transformants to check that >90% of the inserts had the correct size
        Sequence analysis (short run) was performed on 20 clones to confirm their diversity and fungal origin
        Colony picking of 20,000 amp-resistant colonies was carried out into 96-well microtiter plates containing TY medium+100 μg/ml ampicillin
    
    


The 20.000 clones were replicated into 96-well microtiter plates. The ordered libraries are stored as glycerol stocks at −80° C.
Generation of mRNA for cDNA Library Construction
Precultures: A. terreus spores 106-107/ml) were inoculated into 100 ml B medium (2 g/l NH4NO3; 1 g/l MgSo4*7H2O; 0.008 g/l ZnSO4*7H20; 0.015 g/l CuSO4*5H2O; 1.5 ppm FeSO4*5H2O; 0.08 g/l KH2PO4; 10 g/l CaCl2*2H2O, set to pH 3.1 with HCl) containing 20 g/l glucose, and incubated for 24-48 hours at 37° C. at 250 rpm. Production cultures (B medium containing 100 g/l glucose) were inoculated 1/10 (v/v) for 2-days cultivations and 1/25 (v/v) for 3-day cultivations. After 2-3 days cultivation mycelium was harvested, filtered over miracloth, washed with 0.2 M sodium phosphate buffer (pH 6.5), frozen in liquid nitrogen and stored at −80° C.
Isolation of mRNA from A. terreus 


    
    
        grind mycelium with mortar and pestle under liquid nitrogen; add 100 μl β-mercaptoethanol before grinding to inactivate RNAse
        transfer powder to cooled plastic tube (1.0 g per tube); keep mycelium frozen
        add 4 ml Trizol and vortex till homogenous
        add 0.4 ml chloroform and vortex
        centrifuge for 20-30 min. at 3700 rpm, 4° C.
        transfer supernatant to Eppendorf tubes (1.2 ml per tube)
        add 0.7 ml per 1.2 ml supernatant
        centrifuge in eppendorf centrifuge for 15 min. at 14.000 rpm, 4° C.
        wash pellet with 1 ml 70% ethanol
        centrifuge 5 min., 14.000 rpm, 4° C.
        air-dry pellet and resuspend in 0.2 ml water
        store RNA samples at −80° C.

Construction of cDNA Library

The cDNA library was prepared as follows:

        The RNA was run on gel to determine the quality of the sample
        polyT-primed cDNA was prepared from the total RNA provided (RT-PCR reaction using superscript and dT primers
        The cDNA was size fractionated to give fragments of size 1.0-1.5 kb
        The fragments were end-repaired (Lucigen), and ligated into blunt-end pSMART-HC-kan vectors (Lucigen).
        Restriction analysis of 96 clones was performed to check the insert size and the % of transformants which had the correct insert size
        Sequence analysis (short run) of 20 clones was performed to confirm diversity and fungal origin
        5,000 kanamycin-resistant colonies were picked into microtiter plates
    
    


The 5000 cDNA clones were replicated into 96-well microtiter plates. The ordered libraries were stored as glycerol stocks at −80° C.
Construction of the A. terreus Clone-Based Array
PCR fragments were generated from the different clones from the gDNA (20,000 clones) and cDNA (5,000 clones) library by mass 96 well PCR (50 μl/well, Lucigen SMART-SR1/SL1 primers with 5′-C6-aminolinkers, SuperTaq and buffer from HT Biotech. Ltd, dNTP's (Roche 11 969 064 001), pintool dipped template from grown colony plates).
All above PCR products were purified by 96 well precipitation (isopropanol and 96% ethanol wash), speedvac dried, dissolved in 15 μl 3×SSC/well and spotted with quill pins (Telechem SMP3) on CSS100 silylated aldehyde glass slides (Telechem, USA) using a SDDC2 Eurogridder (ESI, Canada). During spotting, aminolinkers of PCR products will covalently link with aldehyde groups of the coated slides.
gDNA and cDNA PCR products were spotted on two separate slides (slide a: 1st 10,000 gDNA's+5000 cDNA's; slide b: 2nd 10,000 gDNA's+same 5000 cDNA's).
For the clone-based array a genomic library was constructed. A total of 20,000 clones containing chromosomal fragments was generated, 90% of which had an average insert size of 1.5-2.5 kb. This resulted in a full genome coverage of 64% (Akopyants, N. S. et al., Mol. Biochem. Parasitol. 113:337-340, 2001).
For the EST-based array a cDNA library of in total 5000 cDNA clones was constructed, 70% of which had an average insert size of 1.0-1.5 kb. This so-called EST-based approach has the advantage that it will be enriched for the genes expressed under the selected (itaconic acid producing) conditions, Moreover, in the EST-based approach per clone (and thus spot) only a single gene is represented in eukaryotes.
The complete micro-array, thus consisting of 20,000 genomic DNA clones and 5,000 cDNA clones was composed of an A and a B glass slide. Both slides contained the same 5,000 cDNA spots. The A and B slide each contained 10,000 of the gDNA spots.
Example 4
Generation of the Different RNA Samples by Fermentation
Materials and Methods Fermentation and mRNA Isolation
Fermentation Conditions of A. terreus 
5-Liter controlled batch fermentations were performed in a New Brunswick Scientific Bioflow 3000 fermentors. The following conditions were used unless stated otherwise:

    
    
        37° C.
        pH start 3.5 set point 2.3
        DO set points Day 1: 75%
        
            Day 2, 3, 4: 50%
            Subsequent days: 25%
        
        
        Preculture: 100 ml of the same medium as used in the fermentation medium (107 spores/ml) in 500 ml Erlenmeyer flask with baffles, overnight, 37° C., 150 rpm
        pH control: 4M KOH (Base), 1.5 M H3PO4(Acid)
        Antifoam: Struktol (Schill & Seilacher)

Fermentation Medium Compositions:

    
    


Per litre: 2.36 g of NH4SO4, 0.11 g of KH2PO4, 2.08 g of MgSO4*7H2O, 0.13 g of CaCl2*2H2O, 0.074 g of NaCl, 0.2 mg of CuSO4*5H2O, 5.5 mg of Fe(III) SO4*7H2O, 0.7 mg of MnCl2*4H2O and 1.3 mg of ZnSO4*7H2O and 100 g of glucose as a carbon source.
All media were prepared in demineralised water.
Isolation of mRNA from A. terreus 
See mRNA isolation protocol described in Example 1
Determination of the Itaconate Concentration by HPLC
5 μl of a 10-times diluted supernatant sample (split ratio 1:3) was separated using a Waters 2695 Separations module on a reversed-phase Develosil 3 μm RP-Aqueous C30 140A column (150×3 mm) (Phenomenex p/n CH0-6001) at 25° C. using the solvent gradient profile (flow rate was 0.4 ml/min) shown in Table 1.







TABLE 1







Solvent gradient of the RP-UV method.










A




(20 mM



NaH2PO4 pH
B


Time
2.25)
(Acetonitril)


(min)
(%)
(%)












0
100
0


10
100
0


15
95
5


20
95
5


21
100
0


30
100
0





Compounds were detected by UV at 210 nm using a Waters 2487 Dual wavelength Absorbance detector (Milford, MA, USA).






Itaconate Productivity

Itaconate productivity at a certain time point was calculated as the slope of the regression line between that particular time point and the time points right before and after that time point. To this end of 6-10 supernatant samples of the different fermentations, the itaconate concentrations were determined by HPLC.
For the transcriptomics approach it is essential to have RNA samples from fermentations that result in the production of different amounts of itaconate. Therefore a literature survey was performed in order to identify medium components and/or physicochemical conditions that affect the amount of itaconate produced by A. terreus. Although many conflicting reports were found regarding the effect that a specific parameter has on itaconic acid production, 4 key overall parameters were identified from this literature survey, i.e. (i) carbon source, (ii) pH, (iii) trace element (i.e. Mn) concentration and (iv) oxygen tension. Fermentations with A. terreus varying principally in these four parameters were performed on a mineral salts medium to ensure that the elemental limitations required for itaconate production would be achieved. Table 2 presents an overview of the fermentations performed in this study.
As shown in Table 2, a considerable variation in the amount of itaconate is produced in this set of fermentations, ranging from almost no itaconate (fermentation #11; pH 4.5) to about 50 g/l itaconate (#8 and #12; O2 set point 25% and 10% respectively).
Of each fermentation 2 to 5 samples were harvested for isolation of mRNA.







TABLE 2







Overview of the fermentations performed in order to generate RNA


samples for transcriptome analysis. The reference fermentation is on


100 g/l glucose, dO2, day 1, 75%, day 2-4, 50%, day 5 and further 25%,


pH start 3.5, set point at 2.3.











Fermentation


Max. Itaconic
Max. Biomass


run
Fermentation
Environmental condition
acid (g/l)
(gDWT/kg)














First Run
1
Glucose (100 g/l) (control)
16.1
12.7



2
Fructose as C-source
8.84
13.7



3
Maltose as C-source
13.9
12.1


Second run
4
Glucose (100 g/l) pH start
25.8
11.6




3.5, set point 2.3 (control)



5
pH set 3.5
8.7
16.5



6
pH start 3.5 no set point
30.6
8.7


Third run
7
Low glucose (30 g/l)
11.1
6.7



8
O2 set point 25%
47.2
12.0



9
5* higher Mn
20.3
13.8


Fourth run
10
Glucose (100 g/l) (control)
26.9
17.9



11
pH set 4.5
0.1
20.4



12
O2 set point 10%
52.9
10.6









From in total 23 fermentation samples mRNA could be isolated. Of 7 samples, mRNA was isolated twice independently. It proved to be especially difficult (impossible) to extract RNA from the samples taken in the stationary phase. A number of samples showed partial degradation of the RNA. Although no mRNA could be isolated from the samples from fermentations #6 and #12, the remaining samples still covered the complete range of itaconate production (Table 3).







TABLE 3







List of 30 mRNA samples from various fermentation conditions that


were used for transcriptome analysis. The samples marked with


asterisk were the samples used for the differential expression


data analysis.

















Itaconic




Sample
Fermentation
RNA
EFT
acid
Produc-
RNA


no.
condition
id
(hours)
(g/l)
tivity
quality
















R3
gluc100
1.3.a
50.3
14.6
0.117
ok


R4
gluc100
1.4.a
74.8
16.1
0.060
ok


R5
fruc100
2.3.a
50.3
 8.2
0.082
ok


R6
fruc100
2.3.b
50.3
 8.2
0.082
ok


R7
fruc100
2.4.a
75.05
 8.6
−0.013
ok


R8
malt100
3.3.a
50.3
7 
0.355
ok


R9
malt100
3.4.a
75
12.1
0.220
ok


R10
pH-i3.5
4.3.a
53.25
25.8
0.146
part








degr


R11
pH-i3.5
4.3.b
53.25
25.8
0.146
part








degr


R12
pH-i3.5
4.4.a
73
24  
−0.153*
ok


R13
pH-c3.5
5.3.a
53.5
 7.5
−0.042
ok


R14
pH-c3.5
5.3.b
53.5
 7.5
−0.042
ok


R15
pH-c3.5
5.4.a
73.25
 7.9
0.035
ok


R16
gluc30
7.2.a
30.25
9 
0.317
ok


R1
gluc30
7.3.a
43.5
10  
0.030
ok


R17
gluc30
7.3.a
43.5
10  
0.030
ok


R18
O2s25%
8.2.a
30.5
36* 
0.824*
ok


R19
O2s25%
8.4.a
78.25
46  
0.029
part








degr


R20
5xMn
9.2.a
30.75
1 
0.194
ok


R21
5xMn
9.2.b
30.75
1 
0.194
ok


R22
5xMn
9.3.a
53.5
10  
0.496
part








degr


R23
5xMn
9.3.b
53.5
10  
0.496
part








degr


R24
5xMn
9.4.a
78.5
19  
0.189
part








degr


R25
5xMn
9.4.b
78.5
19  
0.189
part








degr


R26
5xMn
9.5.a
93.25
20  
0.106
ok


R2
Gluc100
10.3.a
51.5
14.7
0.256
ok


R27
Gluc100
10.3.a
51.5
14.7
0.256
ok


R28
Gluc100
10.4.a
74
19.5
0.085
ok


R29
Gluc100
10.5.a
100.4
22  
0.177
part








degr


R30
Gluc100
10.5.b
100.4
22  
0.177
part








degr


R31
pH4.5
11.3.a
51.5
  0.04*
−0.001
ok


R32
pH4.5
11.4.a
74
  0.05*
0.003
ok









Example 6
Transcriptome Analysis, Data Analysis of the Array Data
Materials and Methods Transcriptome Analysis, Data Normalization and Data Analysis
Labelling of RNA and gDNA
Total RNA's (5 μg/30 μl reaction), isolated from various A. terreus cultures (strain NRRL 1960, BASF) with differential itaconate production, were labelled with amino-allyl-dUTP (0.75 μM aa-dUTP final conc., Sigma A0410), using 3 μl 50 μM oligo p (dT)15 primer (La Roche, 814270), unlabelled dNTP's (added to 1.25 μM final conc. for each dNTP), 2 μl Superscript II Reverse Transcriptase and buffer (Life Technologies, 10297-018: primer annealing 10 min 70° C., transcriptase 180 min 42°). After RNA hydrolysis (3 μl 2.5M NaOH, 30 min 37°, 3 μl 2.5 M HAc) the aa-dUTP labelled cDNA was directly purified (below).
As a reference for correcting slide differences (spotting, labeling-, hybridization- and scan efficiency), gDNA (0.5 μg/reaction) of Aspergillus terreus (strain NRRL 1960, BASF) was labelled with aa-dUTP, using dNTP's (conc. as above), Klenov-DNA Polymerase and buffer (Bioprime kit, Invitrogen 18094-011: primer annealing 5 min 96° C., polymerase 90 min 37 °.
The aa-dUTP-labelled cDNA or gDNA was purified (QIAquick column, Qiagen 28106), speedvac dried, dissolved (4.5 μl 0.1 M Na2CO3), coupled with 4.5 μl Cy5-NHS-ester for cDNA, or 4.5 μl Cy3-NHS-ester for gDNA (Amersham/GE-Healthcare PA25001 or PA23001 respectively, each in 73 μl DMSO) for 60 min at 20° C., diluted with 10 μl of water, and again purified on Autoseq G50 columns (GE-Healthcare 27-5340).
Array Blocking, (pre) hybridization and Image Analysis
Before hybridization with the array produced as described above, slides were blocked (removal surplus of spotted PCR products and blocking of free aldehyde groups) by 3× quickly washing (20° C.) with Prehyb buffer and 45 min incubation (42° C.) in PreHyb buffer (5×SSC, 1% BSA, 0.1% SDS). After 4 washes in water, spotted PCR products were denatured by dipping the slides 5 sec in boiling water and drying them with a N2-gas-pistol.
The Cy5- and Cy3-labelled sample were combined, 8 μl 25 μg/μl yeast tRNA (Invitrogen, 15401-029) and 4 μl 5 μg/μl poly-dA/dT (Amersham 27-7860) were added, the mixture was speed vac dried, dissolved in 160 μl Easyhyb buffer (Roche, 1 796 895), denatured (2 min, 96° C.), cooled to 50° C., applied on a pair of prehybridised slides (a+b, 80 μl/slide) prewarmed at 50° C., covered with a cover slide (Hybri slibs, Mol. Probes. H-18201) and incubated overnight at 42° C. in a humidified hybridization chamber (Corning 2551). Slides were washed (pair a+b in one 50 ml tube, 1× in 1×SSC/0.1% SDS 37° C., 1× in 0.5×SSC 37° C., 2× in 0.2×SSC 20° C.) and dried with N2-gas. All pre-hybridisation buffers were 0.45 μm filtered to reduce dust noise. Slide images of Cy5- and Cy3-fluorescence intensity (ScanArray Express Scanner & Software, Packard Biosc.) were analysed (Imagene 5.6 Software, Biodiscovery) to obtain for each spot signal- and local background value (medians) for the hybridized Cy5-RNA and Cy3-reference gDNA. These values were used for further data analysis.
Array Data Normalization
Before normalization, all low abundant spots having a Signal/Background below 1.5 were removed. Data were normalized using a total cDNA signal correction. For each slide and each spot, the difference between signal and background was calculated for Cy5 and Cy3. Per slide, the sum of the differences was taken for Cy5 and Cy3, and the ratio between these two was used as normalisation factor for that particular slide. All spots (chromosomal and genomic) were normalised using this total cDNA signal.
Data Analysis of the Transcriptomics Data by Differential Expression Analysis
The differential expression value was calculated by dividing the Cy5(RNA)/Cy3 (gDNA) ratio of a spot in the slide with the highest titer or productivity by the Cy5(RNA)/Cy3(gDNA) ratio of that same spot in the slide with the lowest titer or productivity. The samples used for the differential expression analysis are marked in Table 2. The spots were subsequently ranked based on this ratio or, when the ratio was <1, i.e. in the case of down-regulated genes, on 1/ratio.
Sequence Analysis of Spots Selected after Transcriptomics Approach
The relevant clones were selected from the glycerol stocks of the ordered libraries, (gDNA and cDNA library respectively) and cultivated in 96-well microtiter plates. The sequences of the inserts from both the 3′ and the 5′ end were determined by High Throuput (HT) sequencing service.
All RNA samples were labelled with Cy5. Hybridisations were performed with all 30 RNA samples, using Cy3-labeled chromosomal DNA of A. terreus as the reference.
The raw transcriptomics data were shown to be of high quality, based on visual inspection of the arrays after fluorescence scanning. Notably, also the hybridization with the partially degraded RNA samples gave good results.
The normalized data were subsequently combined. As the A. terreus array consisted out of two slides, different strategies of combining the data from the two slides were pursued, making use of the fact that the cDNA clones are present on both the A and B slide:

    
    
        SET 1=mean expression signal of the cDNA clones on slide A and B, take only those spots that give a signal on both the A and B slide
        SET 2=use only the signal of the cDNA spots on the A slide. Spots with a Signal/Background below 1.5 were removed.
        SET 3=use only the signal of the cDNA spots on the B slide. Spots with a Signal/Background below 1.5 were removed.
        SET 4=Combimean cDNA data of both the A and B slide;
        
            i. If both measurement values were zero the combined value was zero;
            ii. If both measurements values were both non-zero, the combined value was equal to the average of the two measurement values;
            iii. If one of the two measurement values was zero and the other measurement value was non-zero, the combined value was equal to the non-zero measurement value.
        
        
        SET 5=SET 1+normalized gDNA spots using the normalization factor calculated based on the cDNA clones.
    
    


The most relevant spots were subsequently identified by differential expression analysis: the expression ratios between the sample with the lowest itaconate titer and the sample with the highest itaconate titer were calculated (see Table 2). As two samples have a low itaconate titer, the differential expression analysis was performed separately with both these reference samples (i.e. sample 3.a. and 4.a). Similarly, also the expression ratios between the samples with the lowest and the samples with the highest itaconate productivity were calculated.
‘Top 20’-ies of the individual data set using the different data analysis approaches were generated. These ‘top-20’-ies were combined, and unique spots were identified (Table 4 and 5). In total 88 spots obtained after the differential analyses (based on 15 models; 5 data sets-2 titer and 1 productivity model) were selected for sequencing.
Of the selected spots, >92% were spots belonging to cDNA clones. Of the differential spots, some 50-75% of the spots were present in the ‘top 20’ of both the itaconate titer and itaconate productivity differentials lists and were mostly upregulated spots, indicating that they might be really relevant for itaconate production.
Following sequence analysis of the 190 selected spots, the genes present on these inserts were identified by performing a homology search using BLAST based on the draft version of the A. terreus genome sequence as available from the BROAD institute (http://www.broad.mit.edu/annotation/fgi/).
Tables 4 and 5 show the results of the genes identified on the 20 highest overall ranking spots identified by differential expression analysis based on titer and productivity, respectively.
Standing out when comparing the highest ranking genes found by differential expression analysis based on productivity versus titer is the cis-aconitate decarboxylase (ATEG—09971.1) which was present on multiple clones in the top 20 rankings, underlining its relevance to the itaconate production phenotype.







TABLE 4







Overall Top 20 Differential expression - itaconic acid titer.













Gene name according to


Rank
Clone ID
Gene locus
(http://www.broad.mit.edu/)













1
AsTeR037B09
ATEG_09971.1
cis-aconitate decarboxylase


2
AsTeR017E03


3
AsTeR008F12
ATEG_09971.1
cis-aconitate decarboxylase


4
AsTeR017E02


5
AsTeR026D10


6
AsTeR020B12


7
AsTeR027F02


8
AsTeR031E12


9
AsTeR041A01


10
AsTeR036C11


11
AsTeR025E11


12
AsTeR008H08


13
AsTeR028C10


14
AsTeR026G08


15
AsTeR009E09
ATEG_09971.1
cis-aconitate decarboxylase


16
AsTeR005D11
ATEG_09971.1
cis-aconitate decarboxylase


17
AsTeR056A03


18
AsTeR010E04


19
AsTeR045C03


20
AsTeR054H08
















TABLE 5







Overall Top 20 Differential expression -


itaconic acid productivity.













Gene name according to


Rank
Clone ID
Gene locus
(http://www.broad.mit.edu/)













1
AsTeR020B12




2
AsTeR031E12


3
AsTeR026D10


4
AsTeR005D11
ATEG_09971.1
cis-aconitate decarboxylase


5
AsTeR017E03


6
AsTeR008F12
ATEG_09971.1
cis-aconitate decarboxylase


7
AsTeR017E02


8
AsTeR037B09
ATEG_09971.1
cis-aconitate decarboxylase


9
AsTeR027F02


10
AsTeR038F06


11
AsTeR008H08


12
AsTeR022C05
ATEG_09971.1
cis-aconitate decarboxylase


13
AsTeR037B09
ATEG_09971.1
cis-aconitate decarboxylase


14
AsTeR004A12


15
AsTeR018E11
ATEG_09971.1
cis-aconitate decarboxylase


16
AsTeR045C03


17
AsTeR045F08


18
AsTeR011A05


19
AsTeR044F02


20
AsTeR041B02









Example 6
Expression of CAD Gene in E. Coli 
In order to unambiguously establish that the ATEG 9971 protein is indeed responsible for CAD activity, an E. coli-codon-usage-optimized synthetic gene of the ATEG 9971 protein was generated synthetically. It was cloned as a BspHI-BamHI fragment into the E. coli expression vector pET19b (Novagen; Cat. No. 69677-3) cut with NotI-BamHI, resulting in vector pET-9971 (see below for nucleotide sequence of vector pET-9971 (SEQ ID NO:42)).







Subsequently E. coli strain BL21 (DE3) was transformed with vector pET-9971 and pET52 (expression vector without an insert) and transformants were cultivated in LB medium and on mineral salts medium (Hellmuth, 1994, J. Biotechnol. 32:289) supplemented with 0.5% glucose, 5 mM MgCl2 and 100 μl/ml ampicillin. Freshly inoculated cultures were grown at 37° C., 250 rpm to an OD600 of 0.5-0.8, incubated on ice for 30 min, after which IPTG was added to a final concentration of 0.2 M. The cultures were subsequently cultivated overnight at 20° C., 250 rpm. Cells were harvested by centrifugation and the medium supernatant was analyzed by HPLC (see example 2).
Moreover, cell extracts were prepared by sonication (2×2 min sonication, setting at 3, output 30-40%-Branson Sonifier 450) in 0.2 M sodium phosphate (pH 6.5), 1 mM Na-EDTA, 1 mM DTT, 1 mM PMSF and 1.0 μg/ml pepstatin A. A cell free extract was obtained by centrifuging the crude extract for 15 min., 10.000 g 4° C. The CAD activity of these cell extracts was determined (Table 6).
IPTG-induced cells contained a distinct band with a molecular weight similar to the CAD protein (FIG. 5). The spent medium of the E. coli expressing the ATEG 9971 showed that these cultures produced up to 0.08 g/l of itaconate (Table 6). Moreover, when cell extracts of these cells were incubated with cis-aconitate itaconate was formed. This was not the case in E. coli containing the original expression vector, or in cells not induced by IPTG (Table 6). This demonstrates that the ATEG 9971 gene indeed codes for cis-aconitate decarboxylase activity.







TABLE 6







Production of itaconate by cell extracts of an E. coli


transformant containing the ATEG 9971 gene in expression


vector pET52 cultivated on different media













Itaconate





produced





from cis-





aconitate





by cell





free




Itaconate
extracts




in
(mg/30




culture
minutes




medium
per mg


Strain
Medium
(mg/l)
protein)













E. coli - pET52
Luria Broth + IPTG
0
0


(empty vector)


E. coli - pET52
Mineral salts medium +
0
0


(empty vector)
IPTG


E. coli - pET-9971
Luria Broth
0
0.2


E. coli - pET-9971
Luria Broth + IPTG
83
18.5


E. coli - pET-9971
Mineral salts medium
0
0.0


E. coli - pET-9971
Mineral salts medium +
56
9.3



IPTG









Example 7
Expression of ATEG—09971.1 in Aspergillus niger 
To establish that introduction of the ATEG 9971 protein is also capable of rendering an naturally non-itaconic acid producing fungal host into a producing organism as PCR generated copy of the gene encoding the ATEG 9971 protein was generated. For this purpose two sets of primers were generated as shown below. PCCR amplification based on A. terreus genomic DNA (SEQ ID NO:23) resulted in the isolation of PCR fragments from which the complete coding region of the gene encoding the ATEG 9971 protein, could be isolated as BspHI-BamHI fragments




Overview Cad Primers:





The resulting BspHI—BamHI fragment was cloned into the Aspergillus expression vector pAN52-4 (EMBL accession #Z32699) digested with NcoI—BamHI. In a derivative of this vector also the Aspergillus selection marker amdS was cloned.
Subsequently, an Aspergillus niger strain derived from AB4.1 (van Hartingveldt, W. et al., 1987, Mol. Gen. Genet. 206:71-75) was transformed with the ATEG 7791 expression vector. AmdS transformants resulting for this experiment were purified by single colony purification and retested for their AmdS+ phenotype. In addition colony PCR was carried out on a selection of the AmdS+ transformants using the primers which were used to generate the PCR gene copy, to verify the presence of an intact ATEG 9971 gene copy in these transformants. Several PCR positive transformants and the parental host strain were subsequently cultured in Batch Fermentation in MM medium containing glucose as C-source and Nitrate as N-source (see example 4). Medium samples from the various cultures were analyzed by HPLC (see example 4) for the presence of itaconic acid. In the medium from the strains containing the ATEG 9971 gene itaconic acid was detected.
Example 8
A. terreus Genome Organization
It appears that at least the gene coding for the cis-aconitate decarboxylase (ATEG—09971.1) and the gene encoding the putitative mitochondrial tricarboxylate transporter (ATEG—9970.1) lie in the same cluster in the A. terreus genome (FIG. 6).
Flanking the CAD and the putative mitochondrial tricarboxylate transporter genes is the Major Facilitator Superfamily (MFS) transporter (ATEG—09972.1) that was identified by Partial Least Squares (PLS) biostatistical analysis. MFS transporters are a diverse family of transport proteins, transporting compounds ranging from sugars to organic acids, including dicarboxylic acids. In A. niger some 450 different MFS genes are present. The localization of MFS ATEG—09972.1 and its identification by PLS, suggest that this is the itaconate exporter.
A gene neighbouring CAD, the putative mitochondrial tricarboxylate transporter and the putative itaconate exporter is a putative regulator containing a zinc-finger domain (ATEG—09969.1). This gene was not identified using our transcriptomics approach, but considering its localization it is supposed that it is relevant for itaconic acid synthesis FIG. 6 shows that also the lovastatin pathway genes are located on this cluster, suggesting a link between both pathways which are (mainly) specific for A. terreus.

## Claims

1. A method for the production of itaconic acid comprising providing to a suitable host cell a recombinant expression system for a nucleic acid molecule encoding the enzyme cis-aconitic acid decarboxylase (CAD) wherein said host cell does not naturally produce itaconic acid or produces itaconic acid only minimally.

2. A method of claim 1, wherein the nucleic acid molecule encodes a CAD protein comprising an amino acid sequence which has an identity of at least 95% with the amino acid sequence of FIG. 2B (SEQ ID NO:2) and which protein exhibits cis-aconitic acid decarboxylase activity.

3. The method of claim 1, wherein said suitable host cell is a citrate producing micro-organism.

4. The method of claim 1, wherein said host is also provided with a nucleic acid molecule encoding a protein that transports di/tricarboxylic acids from the mitochondrion.

5. The method of claim 1, wherein the expression of the zinc-finger regulator protein encoded by the nucleic acid present in ATEG—09969.1 (SEQ ID NOS:17-18) is modulated in said host.

6. The method of claim 1, wherein said host is also provided with a nucleic acid molecule encoding an itaconate transporting Major Facilitator Superfamily Transporter (MFST).

7. The method of claim 3 wherein the microorganism is Aspergillus niger, Aspergillus itaconicus, Yarrowia lipolytica, Ustilago zeae, Candida sp., Rhodotorula sp., Pseudozyma Antarctica, E. coli or Saccharomyces cerevisiae.

8. The method of claim 1 wherein the microorganism is Monascus spp., Penicillium spp., Hypomyces spp., Doratomyces spp., Phoma spp., Eupenicillium spp., Gymnoascus spp., Pichia labacensis, Candida cariosilognicola, Paecilomyces varioti, Scopulariopsis brevicaulis or Trichoderma spp.